title: CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data.
abstract: The full understanding of the mechanisms underlying transcriptional regulatory networks requires unravelling of complex causal relationships. Genome high-throughput technologies produce a huge amount of information pertaining gene expression and regulation; however, the complexity of the available data is often overwhelming and tools are needed to extract and organize the relevant information. This work starts from the assumption that the observation of co-occurrent events (in particular co-localization, co-expression and co-regulation) may provide a powerful starting point to begin unravelling transcriptional regulatory networks. Co-expressed genes often imply shared functional pathways; co-expressed and functionally related genes are often co-localized, too; moreover, co-expressed and co-localized genes are also potential targets for co-regulation; finally, co-regulation seems more frequent for genes mapped to proximal chromosome regions. Despite the recognized importance of analysing co-occurrent events, no bioinformatics solution allowing the simultaneous analysis of co-expression, co-localization and co-regulation is currently available. Our work resulted in developing and valuating CluGene, a software providing tools to analyze multiple types of co-occurrences within a single interactive environment allowing the interactive investigation of combined co-expression, co-localization and co-regulation of genes. The use of CluGene will enhance the power of testing hypothesis and experimental approaches aimed at unravelling transcriptional regulatory networks. The software is freely available at http://bioinfolab.unipg.it/.
authors.affiliation: Department of Biological Sciences, Imperial College London, London, United Kingdom.
authors.forename: Tania
authors.initials: T
authors.lastname: Dottorini
authors.forename: Pietro
authors.initials: P
authors.lastname: Palladino
authors.forename: Nicola
authors.initials: N
authors.lastname: Senin
authors.forename: Tania
authors.initials: T
authors.lastname: Persampieri
authors.forename: Roberta
authors.initials: R
authors.lastname: Spaccapelo
authors.forename: Andrea
authors.initials: A
authors.lastname: Crisanti
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology; D005786:Gene Expression Regulation; D006801:Humans; D014158:Transcription, Genetic